1R9F image
Deposition Date 2003-10-28
Release Date 2004-01-27
Last Version Date 2024-10-30
Entry Detail
PDB ID:
1R9F
Title:
Crystal structure of p19 complexed with 19-bp small interfering RNA
Biological Source:
Source Organism:
Tomato bushy stunt virus (Taxon ID: 12145)
(Taxon ID: )
Method Details:
Experimental Method:
Resolution:
1.85 Å
R-Value Free:
0.23
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
H 3 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Core protein P19
Gene (Uniprot):ORF4
Mutations:L144M, L147M
Chain IDs:C (auth: A)
Chain Length:136
Number of Molecules:1
Biological Source:Tomato bushy stunt virus
Polymer Type:polyribonucleotide
Molecule:5'-R(*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP*AP*UP*U)-3'
Chain IDs:A (auth: B)
Chain Length:21
Number of Molecules:1
Biological Source:
Polymer Type:polyribonucleotide
Molecule:5'-R(*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP*AP*CP*GP*UP*U)-3'
Chain IDs:B (auth: C)
Chain Length:21
Number of Molecules:1
Biological Source:
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
MSE C MET SELENOMETHIONINE
Ligand Molecules
Primary Citation
Recognition of small interfering RNA by a viral suppressor of RNA
Nature 426 874 878 (2003)
PMID: 14661029 DOI: 10.1038/nature02213

Abstact

RNA silencing (also known as RNA interference) is a conserved biological response to double-stranded RNA that regulates gene expression, and has evolved in plants as a defence against viruses. The response is mediated by small interfering RNAs (siRNAs), which guide the sequence-specific degradation of cognate messenger RNAs. As a counter-defence, many viruses encode proteins that specifically inhibit the silencing machinery. The p19 protein from the tombusvirus is such a viral suppressor of RNA silencing and has been shown to bind specifically to siRNA. Here, we report the 1.85-A crystal structure of p19 bound to a 21-nucleotide siRNA, where the 19-base-pair RNA duplex is cradled within the concave face of a continuous eight-stranded beta-sheet, formed across the p19 homodimer interface. Direct and water-mediated intermolecular contacts are restricted to the backbone phosphates and sugar 2'-OH groups, consistent with sequence-independent p19-siRNA recognition. Two alpha-helical 'reading heads' project from opposite ends of the p19 homodimer and position pairs of tryptophans for stacking over the terminal base pairs, thereby measuring and bracketing both ends of the siRNA duplex. Our structure provides an illustration of siRNA sequestering by a viral protein.

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Primary Citation of related structures